This study investigated the potential costs of acclimatization to warmer temperatures in the reef coral Acropora millepora and its symbiotic algae. Field and laboratory experiments found that A. millepora colonies with thermally tolerant symbiont type D grew more slowly than those with sensitive type C2 under normal temperatures. Growth was severely reduced for over 18 months after a bleaching event for all colony types. The stresses of heat damage and symbiont changes may compound to significantly compromise the growth and resilience of reef-building corals.